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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5F39

Crystal structure of human KDM4A in complex with compound 37

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN A 401

Chain	Residue
A	HIS188
A	GLU190
A	HIS276
A	5UB403
A	HOH512

site_id	AC2
Number of Residues	5
Details	binding site for residue ZN A 402

Chain	Residue
A	CYS308
A	CYS234
A	HIS240
A	CYS306
A	SER307

site_id	AC3
Number of Residues	12
Details	binding site for residue 5UB A 403

Chain	Residue
A	TYR132
A	TYR177
A	PHE185
A	HIS188
A	GLU190
A	LYS206
A	TRP208
A	LYS241
A	HIS276
A	ZN401
A	DMS405
A	HOH512

site_id	AC4
Number of Residues	3
Details	binding site for residue DMS A 404

Chain	Residue
A	TYR59
A	ARG98
A	PHE202

site_id	AC5
Number of Residues	6
Details	binding site for residue DMS A 405

Chain	Residue
A	GLY170
A	TYR177
A	GLU190
A	SER288
A	THR289
A	5UB403

site_id	AC6
Number of Residues	3
Details	binding site for residue DMS A 406

Chain	Residue
A	THR83
A	SER230
A	THR243

site_id	AC7
Number of Residues	3
Details	binding site for residue DMS A 407

Chain	Residue
A	ASN137
A	GLY138
A	THR139

site_id	AC8
Number of Residues	5
Details	binding site for residue ZN B 401

Chain	Residue
B	HIS188
B	GLU190
B	HIS276
B	5UB403
B	HOH516

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN B 402

Chain	Residue
B	CYS234
B	HIS240
B	CYS306
B	CYS308

site_id	AD1
Number of Residues	12
Details	binding site for residue 5UB B 403

Chain	Residue
B	TYR132
B	TYR177
B	PHE185
B	HIS188
B	GLU190
B	LYS206
B	TRP208
B	LYS241
B	HIS276
B	ZN401
B	HOH516
B	HOH542

site_id	AD2
Number of Residues	6
Details	binding site for residue DMS B 404

Chain	Residue
B	GLY170
B	TYR177
B	GLU190
B	SER288
B	THR289
B	ASN290

site_id	AD3
Number of Residues	7
Details	binding site for residue DMS B 405

Chain	Residue
B	THR83
B	PHE227
B	SER230
B	PHE237
B	MET242
B	THR243
B	HOH510

site_id	AD4
Number of Residues	5
Details	binding site for residue ZN C 401

Chain	Residue
C	HIS188
C	GLU190
C	HIS276
C	5UB403
C	HOH520

site_id	AD5
Number of Residues	4
Details	binding site for residue ZN C 402

Chain	Residue
C	CYS234
C	HIS240
C	CYS306
C	CYS308

site_id	AD6
Number of Residues	12
Details	binding site for residue 5UB C 403

Chain	Residue
C	TYR132
C	TYR177
C	PHE185
C	HIS188
C	GLU190
C	LYS206
C	TRP208
C	LYS241
C	HIS276
C	ZN401
C	DMS405
C	HOH520

site_id	AD7
Number of Residues	4
Details	binding site for residue DMS C 404

Chain	Residue
C	TYR59
C	ARG98
C	PHE202
C	PHE283

site_id	AD8
Number of Residues	5
Details	binding site for residue DMS C 405

Chain	Residue
C	SER288
C	5UB403
C	GLY170
C	TYR175
C	TYR177

site_id	AD9
Number of Residues	4
Details	binding site for residue DMS C 406

Chain	Residue
C	ASN137
C	GLY138
C	THR139
C	HOH552

site_id	AE1
Number of Residues	6
Details	binding site for residue DMS C 408

Chain	Residue
C	ASP193
C	LYS217
C	TYR273
C	TYR299
C	GLN302
C	HIS343

site_id	AE2
Number of Residues	4
Details	binding site for residue ZN D 401

Chain	Residue
D	CYS234
D	HIS240
D	CYS306
D	CYS308

site_id	AE3
Number of Residues	5
Details	binding site for residue ZN D 402

Chain	Residue
D	HIS188
D	GLU190
D	HIS276
D	5UB403
D	HOH504

site_id	AE4
Number of Residues	12
Details	binding site for residue 5UB D 403

Chain	Residue
D	TYR132
D	TYR177
D	PHE185
D	HIS188
D	GLU190
D	LYS206
D	TRP208
D	LYS241
D	HIS276
D	ZN402
D	HOH504
D	HOH561

site_id	AE5
Number of Residues	3
Details	binding site for residue DMS D 404

Chain	Residue
D	TYR59
D	ARG98
D	PHE283

site_id	AE6
Number of Residues	5
Details	binding site for residue DMS D 405

Chain	Residue
D	TYR175
D	TYR177
D	SER288
D	THR289
D	ASN290

site_id	AE7
Number of Residues	3
Details	binding site for residue DMS D 406

Chain	Residue
D	THR83
D	SER230
D	THR243

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:16677698

Chain	Residue	Details
A	TYR132
D	TYR132
D	ASN198
D	LYS206
A	ASN198
A	LYS206
B	TYR132
B	ASN198
B	LYS206
C	TYR132
C	ASN198
C	LYS206

site_id	SWS_FT_FI2
Number of Residues	8
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00538, ECO:0000269\|PubMed:16677698, ECO:0000305\|PubMed:26741168

Chain	Residue	Details
A	HIS188
A	HIS276
B	HIS188
B	HIS276
C	HIS188
C	HIS276
D	HIS188
D	HIS276

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:16677698, ECO:0000305\|PubMed:26741168

Chain	Residue	Details
A	GLU190
B	GLU190
C	GLU190
D	GLU190

site_id	SWS_FT_FI4
Number of Residues	16
Details	BINDING: BINDING => ECO:0007744\|PDB:5F2W, ECO:0007744\|PDB:5F32, ECO:0007744\|PDB:5F37, ECO:0007744\|PDB:5F39, ECO:0007744\|PDB:5F3E, ECO:0007744\|PDB:5F3G, ECO:0007744\|PDB:5F5I

Chain	Residue	Details
A	CYS234
C	HIS240
C	CYS306
C	CYS308
D	CYS234
D	HIS240
D	CYS306
D	CYS308
A	HIS240
A	CYS306
A	CYS308
B	CYS234
B	HIS240
B	CYS306
B	CYS308
C	CYS234

site_id	SWS_FT_FI5
Number of Residues	4
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:B2RXH2

Chain	Residue	Details
A	LYS241
B	LYS241
C	LYS241
D	LYS241

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: N-acetylalanine => ECO:0007744\|PubMed:19413330

Chain	Residue	Details
A	ALA2
B	ALA2
C	ALA2
D	ALA2

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
A	GLY170	hydrogen bond acceptor, steric role
A	TYR177	hydrogen bond donor, steric role
A	HIS188	metal ligand
A	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
A	HIS276	metal ligand
A	SER288	hydrogen bond donor, steric role

site_id	MCSA2
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
B	GLY170	hydrogen bond acceptor, steric role
B	TYR177	hydrogen bond donor, steric role
B	HIS188	metal ligand
B	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
B	HIS276	metal ligand
B	SER288	hydrogen bond donor, steric role

site_id	MCSA3
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
C	GLY170	hydrogen bond acceptor, steric role
C	TYR177	hydrogen bond donor, steric role
C	HIS188	metal ligand
C	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
C	HIS276	metal ligand
C	SER288	hydrogen bond donor, steric role

site_id	MCSA4
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
D	GLY170	hydrogen bond acceptor, steric role
D	TYR177	hydrogen bond donor, steric role
D	HIS188	metal ligand
D	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
D	HIS276	metal ligand
D	SER288	hydrogen bond donor, steric role

222624

PDB entries from 2024-07-17

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